Referenced by add_scores(), analyze_interface_test(), append_fold_tree_to_file(), InterfaceStrandFinderMover.apply(), HolesTrainingDataMover.apply(), RosettaHolesMover.apply(), HBondReporter.apply(), CrystFFTDock.apply(), assign_rigid_body_settings_to_clusters_test(), atom_vdw_test(), balls_pdb(), bp_score_calibrate(), calc_rama_scores(), calc_scores(), calculate_hASA_by_type_and_attractiveE(), calculate_hASA_by_type_and_exposure(), calculate_hASA_by_type_and_nbcount(), calculate_hydrophobic_accessible_surface_area(), calculate_percent_hydrophobic_distribution(), calculate_total_hASA_within_distance_avg_values(), calculate_total_hASA_within_distance_avgresiduevalues_allnbs_conditionalonnumnbs(), calculate_total_hASA_within_distance_exact_hASA_values(), calculate_total_hASA_within_distance_exact_hASA_values_allnbs(), calculate_total_hASA_within_distance_exact_hASA_values_allnbs_exposedornot_conditionalonnumnbs(), calculate_total_hASA_within_distance_miniSASAvalues_allnbs_exposedornot_conditionalonnumnbs(), change_floating_sc_geometry(), chi_stats_test(), numeric::AgglomerativeHierarchicalClusterer.cluster(), cluster_rigid_body_settings_test(), basic::ComparingTracer.ComparingTracer(), compute_intrinsic_deviation(), connectivity_test(), convert(), numeric::alignment.coordinate_array_broadcast_rmsd(), numeric::alignment.coordinate_array_rmsd(), numeric::alignment.coordinate_array_superimpose(), detail.copy(), utility::file.create_blank_file(), MatchSet.cross(), MatchSet.cross_homodimer(), numeric::geometry::hashing::xyzStripeHash.debug_pdb(), delta_chi_correction_test(), dist_matrix_test(), dna_stats(), do_event_prediction(), dock(), doit(), dostuff(), double_helix_test(), dump_clash_pdb(), dump_data(), dump_ddg_pdb(), dump_efactor_pdb(), dump_grid_pdb(), dump_hbond_pdb(), dump_insert_pdb_and_remodel_blueprint(), TCDock.dump_onecomp(), TCDock.dump_pdb(), Bola.dump_pdb(), Link.dump_pdb(), PoseWrap.dump_pdb(), MatchAlignInfo.dump_pdb(), dump_rotamerset_pdb(), dump_table(), dump_water_grid_file(), dumpsym(), each_aa_test(), easy_target_test(), entropy_calculate_test(), detail.find(), Foldptn.Foldptn(), basic_printf_context< OutputIt, Char >.format(), formatter< arg_join< It, Sentinel, Char >, Char >.format(), formatter< detail::bigint >.format(), formatter< tuple_arg_join< Char, T... >, Char >.format_args(), detail.format_decimal(), detail.format_uint(), frag_extract_test(), detail.get_buffer_init(), get_info_test(), get_sc(), go_main(), utility::file.gunzip(), harvest_motifs(), helix_ST(), hessian_estimate(), ik_his4(), numeric::alignment.indexed_coordinate_array_broadcast_rmsd(), initialize_atoms(), initialize_elements(), protocols::abinitio::JumpSpecificAbrelax.insert_template_frags(), interface_residue_ddg(), is_interface_residue(), is_locked(), isctfast(), kono_sarai_zscore(), ligrot_test(), LocalRmsd.LocalRmsd(), main(), MC_run(), mg_pdbstats_test(), my_main(), mydumppdb(), nucleobase_probe_score_test(), one_chain_MC_sampling(), one_chain_ST_MC(), utility::io::izstream.open(), utility::io::ozstream.open(), utility::io::ozstream.open_append(), numeric.operator<<(), ui::task.operator<<(), numeric::kdtree.operator<<(), numeric::kinematic_closure.operator<<(), utility::tag.operator<<(), operator<<(), numeric::random.operator<<(), output_backbone_stats(), output_caAtomsToConstraint(), output_constraints(), output_local_minima(), output_packstat_pdb(), output_results(), output_strand1_strand2_info(), output_stuff(), output_torsion_list(), output_torsion_M_v_lists(), PairDistance.PairDistance(), SphereSample.pdb_from_level(), pdb_little_motif_test(), phosphate_stats(), PickBAB.PickBAB(), print_cst_file(), print_matrix_to_file(), print_pep_csts(), print_res_freqs(), print_scorefxn(), rb_entropy_test(), register_options(), reverse_convert(), reverse_rbs_test(), rhiju_pdbstats(), rna_sequence_recovery_metrics(), run(), ScoreFragmentSetMover.run(), run_3bpy(), run_diiron_glu(), run_m8(), run_pep_prep(), run_tyr_his(), run_zn2his(), RunPepSpec(), Sasa.Sasa(), utility.save_crash_report_to_file(), ui::task.save_project(), score_clustered_frags(), utility::tag::Tag.setOption(), setup_mask(), basic::resource_manager::locator::FileSystemResourceLocator.show(), sicdock_thread_num(), sicfast(), simple_rotamer_recovery(), sugar_geometry_RNA_test(), test(), test_kc(), test_kc2(), NodeTest.test_node_serialization(), test_PCA_eigen(), NodeTest.test_project_serialization(), NodeTest.test_task_serialization(), tf_specificity_test(), basic::TracerToFile.TracerToFile(), two_base_pairs_via_loop_closure_test(), vec2str(), detail.vformat_to(), detail.write(), write_checkpoint(), write_distances(), write_for_resnum(), detail.write_significand(), numeric.write_tensor_to_file(), numeric.write_tensor_to_file_without_json(), MatchSet.write_to_file(), utility::io.write_vector(), and CrystFFTDock.writeMRC().
